bims-apauto Biomed News
on Apoptosis and autophagy
Issue of 2021‒02‒21
twelve papers selected by
Su Hyun Lee
Seoul National University
  1. Identification of Novel Lipid Droplet Factors that Regulate Lipophagy and Cholesterol Efflux in Macrophage Foam Cells.
  2. Regulation of Autophagy Enzymes by Nutrient Signaling.
  3. PFKP facilitates Atg4B phosphorylation during amino acid deprivation-induced autophagy.
  4. Resveratrol promotes lysosomal function via ER calcium-dependent TFEB activation to ameliorate lipid accumulation.
  5. Reduction of autophagosome overload attenuates neuronal cell death after traumatic brain injury.
  6. The ATG4 protease integrates redox and stress signals to regulate autophagy.
  7. Centrosome amplification mediates small extracellular vesicle secretion via lysosome disruption.
  8. Regulation of autophagy by high- and low-risk human papillomaviruses.
  9. Autophagy buffers Ras-induced genotoxic stress enabling malignant transformation in keratinocytes primed by human papillomavirus.
  10. The functions of autophagy at the tumour-immune interface.
  11. Non-canonical autophagy functions of ATG16L1 in epithelial cells limit lethal infection by influenza A virus.
  12. Functional expression and purification of recombinant full-length human ATG7 protein with HIV-1 Tat peptide in Escherichia coli.
  1. Autophagy. 2021 Feb 16.
    Identification of Novel Lipid Droplet Factors that Regulate Lipophagy and Cholesterol Efflux in Macrophage Foam Cells.
    Sabrina Robichaud, Garrett Fairman, Viyashini Vijithakumar, Esther Mak, David P Cook, Alexander R Pelletier, Sylvain Huard, Barbara C Vanderhyden, Daniel Figeys, Mathieu Lavallée-Adam, Kristin Baetz, Mireille Ouimet.
      Macrophage autophagy is a highly anti-atherogenic process that promotes the catabolism of cytosolic lipid droplets (LDs) to maintain cellular lipid homeostasis. Selective autophagy relies on tags such as ubiquitin and a set of selectivity factors including selective autophagy receptors (SARs) to label specific cargo for degradation. Originally described in yeast cells, 'lipophagy' refers to the degradation of LDs by autophagy. Yet, how LDs are targeted for autophagy is poorly defined. Here, we employed mass spectrometry to identify lipophagy factors within the macrophage foam cell LD proteome. In addition to structural proteins (e.g., PLIN2), metabolic enzymes (e.g., ACSL) and neutral lipases (e.g., PNPLA2), we found the association of proteins related to the ubiquitination machinery (e.g., AUP1) and autophagy (e.g., HMGB, YWHA/14-3-3 proteins). The functional role of candidate lipophagy factors (a total of 91) was tested using a custom siRNA array combined with high-content cholesterol efflux assays. We observed that knocking down several of these genes, including Hmgb1, Hmgb2, Hspa5, and Scarb2, significantly reduced cholesterol efflux, and SARs SQSTM1/p62, NBR1 and OPTN localized to LDs, suggesting a role for these in lipophagy. Using yeast lipophagy assays, we established a genetic requirement for several candidate lipophagy factors in lipophagy, including HSPA5, UBE2G2 and AUP1. Our study is the first to systematically identify several LD-associated proteins of the lipophagy machinery, a finding with important biological and therapeutic implications. Targeting these to selectively enhance lipophagy to promote cholesterol efflux in foam cells may represent a novel strategy to treat atherosclerosis.
    Keywords:  Autophagy; cholesterol efflux; lipid droplet; lipolysis; lipophagy; macrophage foam cell
    DOI:  https://doi.org/10.1080/15548627.2021.1886839
  2. Trends Biochem Sci. 2021 Feb 13. pii: S0968-0004(21)00020-7. [Epub ahead of print]
    Regulation of Autophagy Enzymes by Nutrient Signaling.
    Karyn E King, Truc T Losier, Ryan C Russell.
      Autophagy is the primary catabolic program of the cell that promotes survival in response to metabolic stress. It is tightly regulated by a suite of kinases responsive to nutrient status, including mammalian target of rapamycin complex 1 (mTORC1), AMP-activated protein kinase (AMPK), protein kinase C-α (PKCα), MAPK-activated protein kinases 2/3 (MAPKAPK2/3), Rho kinase 1 (ROCK1), c-Jun N-terminal kinase 1 (JNK), and Casein kinase 2 (CSNK2). Here, we highlight recently uncovered mechanisms linking amino acid, glucose, and oxygen levels to autophagy regulation through mTORC1 and AMPK. In addition, we describe new pathways governing the autophagic machinery, including the Unc-51-like (ULK1), vacuolar protein sorting 34 (VPS34), and autophagy related 16 like 1 (ATG16L1) enzyme complexes. Novel downstream targets of ULK1 protein kinase are also discussed, such as the ATG16L1 subunit of the microtubule-associated protein 1 light chain 3 (LC3)-lipidating enzyme and the ATG14 subunit of the VPS34 complex. Collectively, we describe the complexities of the autophagy pathway and its role in maintaining cellular nutrient homeostasis during times of starvation.
    Keywords:  AMPK; ATG complexes; amino acids; glucose; mTORC1; oxygen
    DOI:  https://doi.org/10.1016/j.tibs.2021.01.006
  3. Cell Signal. 2021 Feb 16. pii: S0898-6568(21)00044-9. [Epub ahead of print] 109956
    PFKP facilitates Atg4B phosphorylation during amino acid deprivation-induced autophagy.
    Xiuzhi Li, Lingling Sun, Guokai Yan, Xianghua Yan.
      Atg4B facilitates autophagy by promoting autophagosome maturation through the reversible lipidation and delipidation of LC3. Recent reports have shown that phosphorylation of Atg4B regulates its activity and LC3 processing, leading to modulate autophagy activity. However, the mechanism about how Atg4B phosphorylation is regulated by amino acid deprivation is unclear. Here, we combined the tandem affinity purification with mass spectrometry (MS) to identify the Atg4B-interacting proteins including its well-known partner gamma-aminobutyric acid receptor-associated protein (GABARAP, a homolog of LC3) and phosphofructokinase 1 platelet isoform (PFKP). Further immunoprecipitation assays showed that amino acid deprivation strengthened the interaction between Atg4B and PFKP. By genetic depletion of PFKP using CRISPR/Cas9, we uncovered that PFKP KO reduced degradation of LC3-II and p62 due to a partial block in autophagic flux. MS analysis of Flag-tagged Atg4B identified phosphorylation of Atg4B serine 34 residue (S34) and PFKP serine 386 residue (S386) under amino acid deprivation condition. In vitro kinase assay validated that PFKP functioning as a protein kinase phosphorylated Atg4B at S34. This phosphorylation could enhance Atg4B activity and p62 degradation. In addition, PFKP S386 phosphorylation abundance correlates with Atg4B S34 phosphorylation abundance and autophagy in HEK293T cells. In brief, our findings described that PFKP, a rate-limiting enzyme in the glycolytic pathway, functions as a protein kinase for Atg4B to regulate Atg4B activity and autophagy under amino acid deprivation condition.
    Keywords:  Amino acid deprivation; Atg4B; Autophagy; PFKP; Phosphorylation
    DOI:  https://doi.org/10.1016/j.cellsig.2021.109956
  4. Biochem J. 2021 Feb 19. pii: BCJ20200676. [Epub ahead of print]
    Resveratrol promotes lysosomal function via ER calcium-dependent TFEB activation to ameliorate lipid accumulation.
    Rong Shao, Jiahui Shi, Kaili Du, Na Wang, Weijie Cai, Siyu Liu, Zongxian Ding, Yihan Wang, Dan Li.
      Abnormal lipid accumulation is associated to the development of metabolic diseases such as hepatic steatosis and lipid storage diseases. Pharmacological agents that can attenuate lipid accumulation therefore have therapeutic potentials for these diseases. Resveratrol (RSV), a natural active substance found in fruits and nuts, has been reported to effectively reduce the intracellular lipid accumulation, but the underlying mechanisms of RSV remain elusive. Here, we show that RSV triggers an endoplasmic reticulum (ER)- Ca2+ signaling that activates transcriptional factor EB (TFEB), a master transcriptional regulator of autophagic and lysosomal biogenesis. Moreover, RSV activates protein phosphatase 2A (PP2A), which binds and dephosphorylates TFEB, promoting its nuclear translocation and the expression of TFEB target genes required for autophagosome and lysosomal biogenesis. Notably, genetic inhibition of TFEB significantly ameliorates RSV-mediated lipid clearance. Taken together, these data link RSV-induced ER calcium signaling, PP2A and TFEB activation to promote autophagy and lysosomal function, by which RSV may trigger a cellular self-defense mechanism that effectively mitigate lipid accumulation commonly associated with many metabolic diseases.
    Keywords:  Lysosome; PP2A; Resveratrol; TFEB
    DOI:  https://doi.org/10.1042/BCJ20200676
  5. Neuroscience. 2021 Feb 15. pii: S0306-4522(21)00080-4. [Epub ahead of print]
    Reduction of autophagosome overload attenuates neuronal cell death after traumatic brain injury.
    Xingyun Quan, Li Song, Xiaomei Zheng, Shenjie Liu, Huaqiang Ding, Sijing Li, Guanghui Xu, Xin Li, Liang Liu.
      Previous studies have shown that alterations in autophagy-related proteins exist extensively after traumatic brain injury (TBI). However, whether autophagy is enhanced or suppressed by TBI remains controversial. In our study, a controlled cortical impact was used to establish a model of moderate TBI in rats. We found that a significant increase in protein levels of LC3-II and SQSTM1 in the injured cortex group. However, there were no significant differences in protein levels of VPS34, Beclin-1, and phosphor-ULK1, which are the promoters of autophagy. Lysosome dysfunction after TBI might lead to autophagosome accumulation. In addition, the highly specific autophagy inhibitor SAR405 administration reduced TBI-induced apoptosis-related protein cleaved caspase-3 and cleaved caspase-9 levels in the ipsilateral cortex, as well as brain edema and neurological defects accessed by mNSS. Furthermore, chloroquine treatment reversed the beneficial effects of SAR405 by increasing the accumulation of autophagosomes. Finally, our data showed that autophagy inhibition by VPS34 gene knockout method attenuated cell death after TBI. Our findings indicate that impaired autophagosome degradation is involved in the pathological reaction after TBI, and the inhibition of autophagy contributes to attenuate neuronal cell death and functional defects.
    Keywords:  SAR405; VPS34; autophagosome; autophagy; neuronal cell death; traumatic brain injury
    DOI:  https://doi.org/10.1016/j.neuroscience.2021.02.007
  6. J Exp Bot. 2021 Feb 15. pii: erab063. [Epub ahead of print]
    The ATG4 protease integrates redox and stress signals to regulate autophagy.
    María Esther Pérez-Pérez, Stéphane D Lemaire, José Luis Crespo.
      Autophagy is a highly conserved degradative pathway that ensures cellular homeostasis through the removal of damaged or useless intracellular components including proteins, membranes or even entire organelles. A main hallmark of autophagy is the biogenesis of autophagosomes, double membrane vesicles that engulf and transport to the vacuole the material to be degraded and recycled. The formation of autophagosomes responds to integrated signals produced as consequence of metabolic reactions or different types of stress and is mediated by the coordinated action of core autophagy-related (ATG) proteins. ATG4 is a key Cys-protease with a dual function in both ATG8 lipidation and free ATG8 recycling whose balance is crucial for proper biogenesis of the autophagosome. ATG4 is conserved in the green lineage and its regulation by different post-translational modifications has been reported in the model systems Chlamydomonas reinhardtii and Arabidopsis thaliana. In this review, we discuss the major role of ATG4 in the integration of stress and redox signals that regulate autophagy in algae and plants.
    Keywords:  ATG4; Chlamydomonas; ROS; autophagy; microalga; plant; protease; redox regulation; stress
    DOI:  https://doi.org/10.1093/jxb/erab063
  7. Curr Biol. 2021 Feb 09. pii: S0960-9822(21)00061-0. [Epub ahead of print]
    Centrosome amplification mediates small extracellular vesicle secretion via lysosome disruption.
    Sophie D Adams, Judit Csere, Gisela D'angelo, Edward P Carter, Maryse Romao, Teresa Arnandis, Martin Dodel, Hemant M Kocher, Richard Grose, Graça Raposo, Faraz Mardakheh, Susana A Godinho.
      Bidirectional communication between cells and their surrounding environment is critical in both normal and pathological settings. Extracellular vesicles (EVs), which facilitate the horizontal transfer of molecules between cells, are recognized as an important constituent of cell-cell communication. In cancer, alterations in EV secretion contribute to the growth and metastasis of tumor cells. However, the mechanisms underlying these changes remain largely unknown. Here, we show that centrosome amplification is associated with and sufficient to promote small extracellular vesicle (SEV) secretion in pancreatic cancer cells. This is a direct result of lysosomal dysfunction, caused by increased reactive oxygen species (ROS) downstream of extra centrosomes. We propose that defects in lysosome function could promote multivesicular body fusion with the plasma membrane, thereby enhancing SEV secretion. Furthermore, we find that SEVs secreted in response to amplified centrosomes are functionally distinct and activate pancreatic stellate cells (PSCs). These activated PSCs promote the invasion of pancreatic cancer cells in heterotypic 3D cultures. We propose that SEVs secreted by cancer cells with amplified centrosomes influence the bidirectional communication between the tumor cells and the surrounding stroma to promote malignancy.
    Keywords:  PDAC; ROS; cancer; centrosome amplification; exosomes; extracellular vesicles; invasion; lysosomes; multivesicular bodies; stellate cells
    DOI:  https://doi.org/10.1016/j.cub.2021.01.028
  8. Rev Med Virol. 2020 Sep 17. e2169
    Regulation of autophagy by high- and low-risk human papillomaviruses.
    Ana Karina Aranda-Rivera, Alfredo Cruz-Gregorio, Alfredo Briones-Herrera, José Pedraza-Chaverri.
      While high-risk human papillomavirus (HR-HPV) infection is related to the development of cervical, vulvar, anal, penile and oropharyngeal cancer, low-risk human papillomavirus (LR-HPV) infection is implicated in about 90% of genital warts, which rarely progress to cancer. The carcinogenic role of HR-HPV is due to the overexpression of HPV E5, E6 and E7 oncoproteins which target and modify cellular proteins implicated in cell proliferation, apoptosis and immortalization. LR-HPV proteins also target and modify some of these processes; however, their oncogenic potential is lower than that of HR-HPV. HR-HPVs have substantial differences with LR-HPVs such as viral integration into the cell genome, induction of p53 and retinoblastoma protein degradation, alternative splicing in HR-HPV E6-E7 open reading frames, among others. In addition, LR-HPV can activate the autophagy process in infected cells while HR-HPV infection deactivates it. However, in cancer HR-HPV might reactivate autophagy in advance stages. Autophagy is a catabolic process that maintains cell homoeostasis by lysosomal degradation and recycling of damaged macromolecules and organelles; nevertheless, depending upon cellular context autophagy may also induce cell death. Therefore, autophagy can contribute either as a promotor or as a suppressor of tumours. In this review, we focus on the role of HR-HPV and LR-HPV in autophagy during viral infection and cancer development. Additionally, we review key regulatory molecules such as microRNAs in HPV present during autophagy, and we emphasize the potential use of cancer treatments associated with autophagy in HPV-related cancers.
    Keywords:  HPV proteins; autophagy; high-risk HPV (HR-HPV); low-risk HPV (LR-HPV); microRNAs; treatments
    DOI:  https://doi.org/10.1002/rmv.2169
  9. Cell Death Dis. 2021 Feb 18. 12(2): 194
    Autophagy buffers Ras-induced genotoxic stress enabling malignant transformation in keratinocytes primed by human papillomavirus.
    Eduardo Cararo-Lopes, Matheus H Dias, Marcelo S da Silva, Julianna D Zeidler, Alexandre T Vessoni, Marcelo S Reis, Enrique Boccardo, Hugo A Armelin.
      Malignant transformation involves an orchestrated rearrangement of cell cycle regulation mechanisms that must balance autonomic mitogenic impulses and deleterious oncogenic stress. Human papillomavirus (HPV) infection is highly prevalent in populations around the globe, whereas the incidence of cervical cancer is 0.15%. Since HPV infection primes cervical keratinocytes to undergo malignant transformation, we can assume that the balance between transforming mitogenic signals and oncogenic stress is rarely attained. We showed that highly transforming mitogenic signals triggered by HRasG12V activity in E6E7-HPV-keratinocytes generate strong replication and oxidative stresses. These stresses are counteracted by autophagy induction that buffers the rapid increase of ROS that is the main cause of genotoxic stress promoted by the oncoprotein. As a result, autophagy creates a narrow window of opportunity for malignant keratinocytes to emerge. This work shows that autophagy is crucial to allow the transition of E6E7 keratinocytes from an immortalized to a malignant state caused by HRasG12V.
    DOI:  https://doi.org/10.1038/s41419-021-03476-3
  10. J Cell Mol Med. 2021 Feb 18.
    The functions of autophagy at the tumour-immune interface.
    Xiaobo Luo, Yan Qiu, Palani Dinesh, Wang Gong, Lu Jiang, Xiaodong Feng, Jing Li, Yuchen Jiang, Yu L Lei, Qianming Chen.
      Autophagy is frequently induced in the hypoxic tumour microenvironment. Accumulating evidence reveals important functions of autophagy at the tumour-immune interface. Herein, we propose an update on the roles of autophagy in modulating tumour immunity. Autophagy promotes adaptive resistance of established tumours to the cytotoxic effects of natural killer cells (NKs), macrophages and effector T cells. Increased autophagic flux in tumours dampen their immunogenicity and inhibits the expansion of cytotoxic T lymphocytes (CTLs) by suppressing the activation of STING type I interferon signalling (IFN-I) innate immune sensing pathway. Autophagy in suppressive tumour-infiltrating immune subsets maintains their survival through metabolic remodelling. On the other hand, autophagy is involved in the antigen processing and presentation process, which is essential for anti-tumour immune responses. Genetic deletion of autophagy induces spontaneous tumours in some models. Thus, the role of autophagy is context-dependent. In summary, our review has revealed the dichotomous roles of autophagy in modulating tumour immunity. Broad targeting of autophagy may not yield maximal benefits. The characterization of specific genes regulating tumour immunogenicity and innovation in targeted delivery of autophagy inhibitors into certain tumours are among the most urgent tasks to sensitize cold cancers to immunotherapy.
    Keywords:  autophagy; immune cell; tumour cell; tumour immunity
    DOI:  https://doi.org/10.1111/jcmm.16331
  11. EMBO J. 2021 Feb 15. e105543
    Non-canonical autophagy functions of ATG16L1 in epithelial cells limit lethal infection by influenza A virus.
    Yingxue Wang, Parul Sharma, Matthew Jefferson, Weijiao Zhang, Ben Bone, Anja Kipar, David Bitto, Janine L Coombes, Timothy Pearson, Angela Man, Alex Zhekova, Yongping Bao, Ralph A Tripp, Simon R Carding, Yohei Yamauchi, Ulrike Mayer, Penny P Powell, James P Stewart, Thomas Wileman.
      Influenza A virus (IAV) and SARS-CoV-2 (COVID-19) cause pandemic infections where cytokine storm syndrome and lung inflammation lead to high mortality. Given the high social and economic cost of respiratory viruses, there is an urgent need to understand how the airways defend against virus infection. Here we use mice lacking the WD and linker domains of ATG16L1 to demonstrate that ATG16L1-dependent targeting of LC3 to single-membrane, non-autophagosome compartments - referred to as non-canonical autophagy - protects mice from lethal IAV infection. Mice with systemic loss of non-canonical autophagy are exquisitely sensitive to low-pathogenicity IAV where extensive viral replication throughout the lungs, coupled with cytokine amplification mediated by plasmacytoid dendritic cells, leads to fulminant pneumonia, lung inflammation and high mortality. IAV was controlled within epithelial barriers where non-canonical autophagy reduced IAV fusion with endosomes and activation of interferon signalling. Conditional mouse models and ex vivo analysis showed that protection against IAV infection of lung was independent of phagocytes and other leucocytes. This establishes non-canonical autophagy in airway epithelial cells as a novel innate defence that restricts IAV infection and lethal inflammation at respiratory surfaces.
    Keywords:  ATG16L1 WD Domain; cytokine storm; influenza; intrinsic defence; non-canonical autophagy
    DOI:  https://doi.org/10.15252/embj.2020105543
  12. Protein Expr Purif. 2021 Feb 13. pii: S1046-5928(21)00027-9. [Epub ahead of print] 105844
    Functional expression and purification of recombinant full-length human ATG7 protein with HIV-1 Tat peptide in Escherichia coli.
    Guofu Dong, Xi Zhao, Junwang Guo, Lei Ma, Hongmei Zhou, Qi Liu, Xuelong Zhao, Changzhen Wang, Ke Wu.
      The human autophagy-related protein ATG7 (hATG7), an E1-like ubiquitin enzyme, activates two ubiquitin-like proteins, LC3 (Atg8) and Atg12, and promotes autophagosome formation. While hATG7 plays an essential role for the autophagy conjugation system, the production of full-length functional hATG7 in bacterial systems remains challenging. Previous studies have demonstrated that the HIV-1 virus-encoded Tat peptide ('GRKKRRQRRR') can increase the yield and solubility of heterologous proteins. Here, functional full-length hATG7 was expressed using the pET28b-Tat expression vector in the Escherichia coli BL21 (DE3) strain. Recombinant hATG7 protein aggregated as inclusion bodies while expressed with widely used prokaryotic expression plasmids. In contrast, the solubility of Tat-tagged hATG7 increased significantly with prolonged time compared to Tat-free hATG7. The recombinant proteins were purified to >90% homogeneity under native conditions with a single step of affinity chromatography purification. The results of in vitro pull-down and LC3B-I lipidation assays showed that Tat-tagged hATG7 directly interacted with LC3B-I and promoted LC3B-I lipidation, suggesting that Tat-tagged hATG7 has significant catalytic activity. Overall, this study provides a novel method for improving the functional expression of full-length hATG7 in bacterial systems by fusion with the Tat peptide, a process which may be applied in future studies of hATG7 structure and function.
    Keywords:  Escherichia coli; Functional expression; Human ATG7; Tat peptide; autophagy
    DOI:  https://doi.org/10.1016/j.pep.2021.105844
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